Biology subjects

Vendruscolo, M.

Publications and source records attributed to Vendruscolo, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Melanin Suppresses Aβ Aggregation and Toxicity

The aggregation of amyloid-{beta} (A{beta}) peptides into insoluble deposits is a characteristic hallmark of Alzheimer's disease (AD) and related neurodegenerative disorders. While AD is the most common cause of dementia, there are currently no disease-modifying treatments which are both affordable and adverse-free. In this study, we report that melanin, a pigment which is commonly found in nature and is abundant in parts of the human brain, suppresses the aggregation of the 42-amino acid A{beta} variant (A{beta}42). Using biophysical and biochemical techniques, we show that melanin delays A{beta}42 aggregation while also reducing the amount of A{beta}42 that converts into aggregates. Using thioflavin T assays paired with chemical kinetics, we characterised the melanin-induced inhibition of A{beta}42 aggregation in vitro. Using MALDI-MS, we elucidate the molecular basis of this effect by showing that melanin prevents A{beta}42 dimerisation. We then demonstrate that melanin also reverts the aggregation process by dissolving pre-formed A{beta}42 fibrils. Finally, we show that melanin reduces A{beta}42 aggregation and rescues A{beta}42 toxicity in an SH-SY5Y neuroblastoma cell model. Our study shows that melanin disrupts the aggregation and cytotoxicity of A{beta}42, and suggests that compounds derived from human metabolites may offer promising avenues to combat amyloid formation.

biophysics↗

bioRxiv2026

Low-abundance αSyn-112 promotes αSyn-140 aggregation in vitro and forms immunoreactive deposits in Parkinson's disease brain tissue

The aggregation of -synuclein (Syn) is a molecular hallmark of Parkinsons disease (PD) and other synucleinopathies. Understanding the molecular mechanisms that determine the aggregation of this protein may thus facilitate the development of disease-modifying therapies. While Syn is most commonly expressed as a 140-residue protein (Syn-140), recent evidence suggests an involvement of alternatively spliced Syn isoforms in disease onset and progression. Here, we report and characterise the interaction between Syn-140 and the aggregation-prone Syn-112 variant, one of the most abundant Syn splice isoforms. We found that amounts as low as 1% of Syn-112 accelerate the nucleation and aggregation of Syn-140. To further investigate this phenomenon, we employed MALDI-MS and NMR spectroscopy, confirming that Syn-140 and Syn-112 monomers interact strongly with one another. Furthermore, to assess the association of Syn-112 with disease pathology, we performed immunohistochemical staining combined with confocal microscopy on PD brain samples. Thereby, we found an increase in the number as well as the area of Syn-112 immunoreactive aggregates compared to healthy controls. These results illustrate how low-abundance Syn splice isoforms can modulate the aggregation landscape of Syn-140 and in turn contribute to the molecular heterogeneity of synucleinopathies.

biophysics↗

bioRxiv2026

Complex coacervation reshapes the aggregation landscape of tau

Biomolecular condensates are increasingly implicated in protein aggregation, yet their contribution is often reduced to that of concentrating reactants. Whether the phase state of a protein itself changes how it aggregates remains unclear. Using complex coacervates of a tau repeat-domain construct (K12) with heparin, we show that phase separation does not simply accelerate tau aggregation but redirects it along a distinct kinetic regime. Amyloid nucleation and growth are largely associated with the condensed phase, where intact phase-separated mixtures nucleate with a markedly shortened lag phase, whereas the corresponding dilute phase contributes little to overall amyloid formation. Aggregation kinetics in this regime become largely decoupled from total protein concentration. Because phase equilibrium pins the composition of the dense phase, additional tau partitions largely into the coexisting dilute phase without substantially altering the reacting population. This weak concentration dependence provides a kinetic signature of compartmentalized aggregation, and it recurs across chemically distinct coacervates formed with heparin, RNA, and polyglutamate, pointing to a general feature of coacervate-mediated tau assembly rather than a heparin-specific effect. Aggregation within coacervates also yields fibrils with altered morphology and secondary structure, suggesting access to alternative regions of the assembly landscape, and shows reduced sensitivity to bulk pH perturbations. Together, these results show that condensation changes tau aggregation by defining the local reaction environment: phase equilibrium buffers the dense-phase composition, in turn altering aggregation kinetics and the properties of the amyloid formed.

biophysics↗

bioRxiv2026

Preserving Native Cellulose-Xylan Architecture Enables Structure-Property Control in Holocellulose Nanofibrils and High-Performance Sustainable Materials

The hierarchical organization of cellulose microfibrils and their intimate interactions with hemicelluloses such as xylan underpin the exceptional mechanical performance of plant cell walls. However, translating these biological design principles into sustainable nanocellulosic materials remains limited by conventional cellulose nanofibril production routes, which rely on harsh chemical treatments that disrupt the native cellulose-hemicellulose architecture. Here, we present an optimized isolation strategy for holocellulose nanofibrils (hCNFs) that preserves native cellulose structure, xylan substitution and conformation, and cellulose-xylan interactions. Using wild-type Arabidopsis thaliana, a xylan glucuronidation-deficient gux1/2 mutant, and Brassica napus straw as model systems, we systematically elucidate how xylan content and substitution pattern govern nanofibril isolation, interfacial interactions, and macroscopic properties. Two-dimensional 13C magic-angle spinning NMR demonstrates retention of native cellulose glucosyl environments, the presence of two-fold and three-fold helical xylan conformations, and cellulose-associated two-fold helical xylan. Cryogenic transmission electron microscopy reveals fibril widths of [~]3 nm, consistent with elementary cellulose I{beta} microfibrils. We show that xylan glucuronidation regulates colloidal stability, hydration behavior, and interfibrillar cohesion, whereas xylan content controls nanofibrillation efficiency. These multiscale structural features translate directly into moisture sorption, thermal behavior, and mechanical performance. Notably, Brassica napus hCNF films exhibit exceptional strength and extensibility, surpassing many chemically modified CNF systems. This work demonstrates that preserving the native cellulose-hemicellulose architecture enables high-performance, sustainable nanocellulosic materials without chemical reconstruction.

biochemistry↗

bioRxiv2026

Effects of PTMs on Tau Protein Aggregation: Insights from HCG and Atomistic MD Simulations

Post-translational modifications (PTMs) of the tau protein are increasingly recognized as pivotal regulators in the onset and progression of tauopathies, such as Alzheimers disease (AD). To systematically evaluate the structural and functional consequences of specific PTMs, we generated and analyzed seven distinctly modified variants of the tau-K32 construct. These included phosphorylation at Ser202/Thr205, phosphorylation at Ser258/Ser262/Ser356, full phosphorylation at all reported Ser/Thr sites, acetylation at Lys274/Lys281, acetylation at Lys280, full acetylation at all sites, and an unmodified control. Selection of PTM sites was guided by prior experimental literature. By incorporating fully modified tau models, we assessed the global impact of widespread modifications on structural properties and aggregation behavior. Our findings establish a comparative framework for understanding how discrete and cumulative PTMs modulate tau aggregation and provide mechanistic insight into PTM-induced tau dysfunction relevant to neurodegenerative diseases.

biochemistry↗

bioRxiv2026

Does the sequence of a disordered protein encode small molecule binding paths?

Ligand binding to intrinsically disordered proteins resists description in terms of conventional binding pockets, yet it can be analysed as a dynamic process in which ligands move across transient surface interaction sites. Here we characterise a pathway-based representation in which ligand binding is described as a sequence of transitions between residue-defined microstates, enabling ligand-specific effects to be distinguished from intrinsic properties of the peptide conformational ensemble. Using all-atom molecular dynamics simulations of A{beta}42 and the C-terminal region of -synuclein in complex with chemically diverse small molecules, we construct transition matrices that encode ligand movement across the peptide surface and use Markov state models to identify dominant binding pathways and relative binding propensities. Pairwise enrichment-factor and AUC analyses reveal strong conservation of the highest-ranked pathways across chemically diverse ligands, with enrichment factors of 15-45 for the top-ranked states and AUC values typically [≥]0.75, well above random expectation. These dominant pathways are also preserved across changes in pH and temperature, whereas a urea control, included as a non-specific binder, shows reduced enrichment, indicating that ligands primarily modulate pathway weights rather than define the underlying network topology. Ensemble docking across chemically diverse libraries further supports the presence of recurrent ligand-accessible hotspots within the peptide conformational ensemble. Building on this framework, we apply a prospective screening pipeline to A{beta}42, combining MSM-derived hotspots with sequence-based Ligand-Transformer scoring and Gnina docking across 1.66 million compounds, to nominate 19 candidates for prospective experimental evaluation. Together, these results indicate that disordered protein sequences give rise to conformational ensembles that exhibit characteristic binding pathways for small molecules.

biophysics↗

bioRxiv2026

Spatially patterned, spectral single-molecule microscopy

Multicolour and spectrally resolved single-molecule microscopy can reveal molecular interactions, nanoscale environments and dynamics, but usually depends on experimentally complex detection architectures based on beam splitting, spectral dispersion or engineered point spread functions. Here we show that spatially patterned detectors offer a conceptually simpler route to spectral single-molecule imaging. By replacing a conventional monochrome camera with a commercially available colour CMOS detector and fitting the raw detector response directly, we recover both molecular position and spectral fingerprint from a single image without optical splitting, channel registration or demosaicing. We term this approach spatial spectral single-molecule microscopy, or S3M. We show that S3M retains single-molecule sensitivity across the visible spectrum, enables robust spectral multiplexing, and supports applications spanning multicolour single-molecule tracking, single-molecule F&oumlrster resonance energy transfer, multicolour localisation microscopy and spectral PAINT. Although spatial patterning necessarily trades photon efficiency for spectral information, current low noise detectors already provide sufficient performance for a broad range of experiments. Spatially patterned detection therefore establishes a widely accessible strategy for simplified spectral microscopy and single-molecule spectroscopy, and points towards a new class of detector informed photonic measurement schemes for nanoscale imaging.

biophysics↗

bioRxiv2026

Microglia as transcriptional pacemakers of neuronal aging heterogeneity across individuals

Neuronal aging pace varies markedly between individuals, but what drives this variation remains unknown. Using cell-type-specific transcriptomic clocks applied to single-nucleus RNA sequencing data from 226 adults (ages 20-90), we quantified neuronal aging residuals as a donor-dominant phenotype. Variance decomposition revealed that microglial transcriptional programs predict inter-individual variation in neuronal aging residuals, a directional asymmetry consistent with a non-cell-autonomous relationship between microglial states and neuronal aging trajectories. This asymmetry is accompanied by an age-dependent shift from homeostatic to inflammatory microglial dominance beginning in midlife, with inflammatory dominance probability rising from 26% at age 35 to 92% by age 65, replicated in an independent cohort. IFN{gamma} signaling emerges as the dominant microglial program associated with accelerated neuronal aging in late adulthood. Candidate regulators of microglial IFN{gamma} activity (HIF1A, CEBPB, and EZH2) are computationally prioritized as intervention targets warranting functional validation.

neuroscience↗

bioRxiv2026

Metabolostasis failure thresholds are linked with network topology, metabolite solubility, and translational control

Cells maintain metabolite homeostasis (metabolostasis) by buffering fluctuations in metabolite levels, yet the limits of this buffering and the mechanisms underlying metabolic toxicity remain poorly understood. To study this, we systematically overfed metabolites in Saccharomyces cerevisiae and quantified associations with growth inhibition, intracellular aggregation, and multiomic perturbations. We identify metabolite-specific failure thresholds at which amyloid-like aggregates are observed, with graded growth inhibition detectable at sub-threshold concentrations, suggesting toxicity mechanisms beyond transporter saturation. Metabolites with higher network influence and broader pathway participation are associated with higher failure thresholds and smaller pathway disturbances. These patterns are associated with chemical properties and solubility: more soluble metabolites, while broadly tolerated, are associated with localised aggregates at their failure thresholds, whereas less soluble metabolites are associated with larger systemic pathway disruptions. Multiomic integration identifies a two-tiered translational regulatory architecture characterising cellular resilience to metabolic overfeeding. General resilience is associated with transcriptional commitment to resource conservation via attenuation of anabolic pathways. Metabolite-specific defense is characterised by high-magnitude translational regulatory events; for example, engagement of aromatic catabolism under phenylalanine overfeeding and energetic control pathways under glycine overfeeding. Together, our results operationally define metabolostasis as a cellular system associated with constraint of metabolite concentrations, coordination of network and pathway-level regulation, and buffering against amyloid-like aggregation, highlighting how network topology, pathway architecture, and chemical properties are associated with metabolic resilience and toxicity thresholds.

cell biology↗

bioRxiv2026

OmniBind: Proteome-Wide Promiscuity Predictions for Early-Stage Drug Screening

Off-target binding remains a leading cause of drug attrition, yet no method exists for rapidly quantifying small-molecule promiscuity across the human proteome. Here, we define promiscuity as the mean predicted binding affinity over 15,405 human proteins and derive a specificity score combining target affinity with this proteome-wide distribution. To make this assessment tractable at scale, we introduce OmniBind, a message-passing neural network that predicts promiscuity directly from a SMILES string at about a thousand compounds per second, several orders of magnitude faster than proteome-wide profiling. OmniBind promiscuity scores correlate with experimental binding data near assay reproducibility limits. Ranking candidates by specificity rather than affinity alone improves enrichment of approved drugs across all thresholds tested, an advantage robust to the choice of affinity predictor. OmniBind fills an unoccupied niche in the early-stage screening landscape as a fast, proteome-scale complement to traditional safety panels, with accuracy that will scale as the underlying affinity predictors continue to improve.

molecular biology↗

bioRxiv2026

Distinct mechanistic pathways of early tauopathy revealed by MAPT mutations

Tau pathology underlies a broad spectrum of neurodegenerative disorders, collectively termed tauopathies, yet these diseases exhibit striking heterogeneity in their biological mechanisms and clinical outcomes. The basis for this heterogeneity remains poorly understood. Here, we address this question using knock-in mouse models expressing two distinct frontotemporal dementia-associated tau mutations to define how different tau variants drive divergent pathogenic programs in vivo. We find that the two mutations give rise to fundamentally different trajectories of tau pathogenesis. One trajectory is marked by progressive tau hyperphosphorylation and cytoskeletal destabilization occurring in the absence of detectable tau seed formation. In contrast, an alternative trajectory is characterized by tau hypophosphorylation, early seed formation, and alterations in nucleotide metabolism and chromatin organization, without overt cytoskeletal disruption. With aging, tau in this latter pathway transitions to a hyperphosphorylated state and forms mature fibrillar aggregates. Genetic enhancement of {beta}-amyloid selectively accelerates fibril formation, particularly in the model exhibiting early seeding. Together, these findings demonstrate that distinct tau mutations can engage separable pathogenic mechanisms, providing a biological framework for the heterogeneity observed across tauopathies, and highlighting the need for mechanism-informed therapeutic strategies and patient stratification. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/705716v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@11eb652org.highwire.dtl.DTLVardef@153cc53org.highwire.dtl.DTLVardef@8b670eorg.highwire.dtl.DTLVardef@1afaad_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractSchematic representation comparing two trajectories of tau pathology. The S305N mutation promotes a 4R isoform shift, cytoskeletal damage and synapse loss, and accumulation of soluble hyperphosphorylated tau. Tau remains soluble even at old ages. In contrast, the P301S mutation generates hypophosphorylated, seed-competent tau that forms fibrils. The effect of amyloid is slow in the S305N, but results in accelerated acceleration of pathology in the P301S. Figure made with Biorender.com.

neuroscience↗

bioRxiv2026

Metadiffusion: inference-time meta-energy biasing of biomolecular diffusion models

Biomolecular function often depends on conformational ensembles, yet modern diffusion-based structure generators are biased toward the compact conformations prevalent in structural databases, limiting their ability to explore broad conformational landscapes. This work introduces metadiffusion, where an additional meta-energy biasing layer on top of diffusion steers pretrained biomolecular diffusion models through gradient-guided denoising. Without retraining, metadiffusion generates diverse conformational ensembles whose residue-level flexibility patterns closely match molecular dynamics simulations. The method supports three complementary modes: optimisation, steering to user-specified targets, and exploration via inter-sample repulsion. This approach enables controlled exploration of collective variables, enumeration of alternative binding poses across proteins, nucleic acids and ligands, and conformational ensemble generation consistent with SAXS and NMR chemical shifts. Metadiffusion thus provides a practical route to connect diffusion-based structure generation with ensemble-level, experimentally-restrained structural analysis.

bioinformatics↗

bioRxiv2025

Binding Paths: Describing Small Molecule Interactionswith Disordered Proteins via Markov State Models

Disordered proteins are challenging targets for drug discovery because they lack well-defined binding pockets. Although small molecules can form relatively stable complexes with disordered proteins, the highly dynamic nature of these proteins complicates the understanding of their binding mechanism. To address this problem, we analyze the binding of the small molecule 10074-G5 to A{beta}42, which results in the formation of a disordered complex. We describe the binding mechanism in terms of binding paths, which are stochastic trajectories along which small molecule diffuse across disordered protein surfaces, forming transient contacts with overlapping groups of residues. To identify these binding paths, we define them as realizations of a stochastic process defined by a Markov State Model (MSM). The MSM is built from distinct states of the disordered complex and their corresponding transition probabilities, enabling both the dynamic mapping of binding hotspots and targetable regions where static pockets cannot be defined-extending the notion of binding pockets to disordered systems - and the quantitative calculation of binding affinities. The visualization of the MSM via knowledge graphs provides an intuitive representation of the binding paths. We further validated this approach across four additional systems, comprising C-terminal -synuclein with three distinct small-molecule binders, and the full-length peptide (140 residues) with binder fasudil. By generalizing the concept of static binding pockets to dynamic binding paths, our approach rationalizes small-molecule recognition by disordered proteins and establishes a framework for identifying druggable regions on systems that were previously considered intractable, providing insights for future drug design programs.

biophysics↗

bioRxiv2025

Secondary nucleation of α-Synuclein drives Mitochondria dysfunctions and Lewy body formation in Parkinson's Disease

The seeding of -Synuclein (Syn) is a key driver of Lewy pathology propagation in Parkinsons disease (PD) and forms the basis for recent diagnostic advances. However, it remains unclear how the structural and biochemical features of Syn seeds dictate their propagation efficiency, capacity to induce Lewy body formation, and resulting cellular toxicity. Using genetic and idiopathic PD cell models, we map the pathogenic cascade beginning with the seed-driven conversion of endogenous Syn, followed by impaired degradation, mitochondrial dysfunction, and ultimately Lewy body formation. By coupling kinetic modelling of aggregation with functional readouts, we identify secondary nucleation as the predominant mechanism generating toxic Syn aggregation intermediates, identifying the critical process that links seeding to pathology. Extending this framework to PD brain, we quantitatively correlate seeding capacity with the spatiotemporal spread and severity of Lewy pathology, revealing a mechanistic connection between Syn aggregation dynamics and disease progression at molecular, cellular, and anatomical levels. By unifying molecular mechanism with clinicopathological progression, our work identifies catalytic Syn fibrillar seeds as tractable targets for both disease-modifying therapy and biomarker development in PD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/676873v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@1eca299org.highwire.dtl.DTLVardef@a714d4org.highwire.dtl.DTLVardef@1486db5org.highwire.dtl.DTLVardef@1aa895_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISyn fibril-oligomer interplay drives mitochondrial abnormalities and Lewy pathology C_LIO_LIFibrillar Syn catalyse toxic aggregate formations via secondary nucleation C_LIO_LIPhosphorylated Syn evades lysosomal clearance and drives enhanced dysfunctions C_LIO_LISeeding capacity of Syn predicts Lewy pathology burden and disease progression C_LI

neuroscience↗

bioRxiv2025

Microglial activation and alpha-synuclein oligomers drive the early inflammatory phase of Parkinson's disease

Parkinsons disease (PD) is characterised by insoluble -synuclein (Syn) aggregates in Lewy bodies (LBs) within the substantia nigra, with cortical pathology appearing as the disease progresses. Late-stage LB deposition, cellular stress, and neuronal loss obscure disease-driving events, we therefore performed multi-regional transcriptomic and aggregate profiling in early-midstage PD brains (Braak 3-4), where cortical regions are pathologically unaffected. We report neuroimmune activation as an early PD feature, characterised by the expansion of a high-SNCA-expressing microglial state. This robust immune signature occurs prior to LB formation, but is associated with oligomeric Syn within cortical microglia. In hiPSC-derived microglia, both endogenous Syn oligomerisation, and exogenous oligomer uptake, trigger transcriptional reprogramming, characterised by interferon-driven inflammation, antigen presentation, and mitochondrial suppression, closely mirroring the early PD brain. These findings describe mechanisms by which Syn oligomerisation potently initiates early neuroinflammation, highlighting a critical interplay between proteinopathy and immune activation at the earliest stages of disease.

neuroscience↗

bioRxiv2025

α-Synuclein driven cell susceptibility in Parkinson's disease

Early cellular events in Parkinsons disease (PD) remain elusive. While aggregation of -synuclein (Syn) into Lewy bodies marks advanced pathology, smaller Syn oligomers have been implicated in prodromal stages. Here we map Syn oligomers at single-particle resolution in post-mortem brain tissue from Braak stage 3/4 PD cases and matched controls. Quantitative imaging of 9,882 neurons across four regions captured over 112 million Syn oligomers. Mean intracellular -Syn burden was unchanged between groups, but PD samples contained a higher fraction of neurons whose oligomer load exceeded a specific aggregation threshold. We term these aggregation-susceptible cells (ASCs). ASC enrichment in vulnerable regions supports a population-level model in which early pathology arises from a stochastic shift in cellular composition rather than altered Syn aggregation kinetics. This human-tissue, large-scale dataset provides a quantitative framework for detecting ASCs and for testing population-level interventions in PD and related proteinopathies.

neuroscience↗

bioRxiv2025

Structure-based Generation of a Secondary Nucleation Inhibitor in alpha-Synuclein Aggregation Using a Conditional Diffusion Model

The process of -synuclein aggregation results in the formation of amyloid fibrils, which accumulate in the brain of patients affected by Parkinsons disease. Among possible therapeutic strategies to cure this disease, one approach is based on the development of compounds capable of inhibiting -synuclein aggregation. An effective inhibition could be achieved by blocking the nucleation sites on the surface of the amyloid fibrils that are responsible for their autocatalytic proliferation. Here, we report a strategy based on deep learning to achieve this goal, which uses an E(3)-equivariant conditional diffusion model. By using this approach, we designed and tested experimentally candidate small molecules. We found that one of these small molecules acts as a potent inhibitor of secondary nucleation in -synuclein aggregation. These results provide evidence that generative diffusion models offer effective tools for drug design.

biophysics↗

bioRxiv2025

Tracking tau and cellular responses in human iPSC-microglia from uptake to seedable secretion in extracellular vesicles

The templated spread of tau aggregates in tauopathies has been attributed to neuron-to- neuron spread, but microglia have also been implicated through mouse studies. Here we examine in detail the uptake, processing, release and seeding of tau using human iPS- derived microglia (iMGL). We show that tau is taken up by iMGL via LRP1 and heparan sulfate proteoglycans, with a role for LRRK2 in LRP1 trafficking, and that phagocytosed fibrils can escape into the cytoplasm. Monomeric tau has minimal effects on iMGL, but recombinant or brain-derived tau fibrils induce a shift towards chemokine and interferon response subtypes, alongside downregulation of homeostatic and MHC genes. Endogenous tau protein is undetectable in iMGL, and monomeric internalised tau is digested to completion, but fibrillar tau is more resistant to degradation and becomes phosphorylated on two specific residues. Finally, fibrillar tau is released by iMGL, visualized within extracellular vesicles by cryo-EM, and can seed tau aggregation in downstream neurons.

cell biology↗